A mass spectrometric investigation was made of the fragmentation of protonated peptide ions produced by matrix-assisted laser desorption/ionization (MALDI) in an ion source external to a quadrupole ion trap mass analyzer. Highly preferential cleavage was detected at peptide bonds adjacent to aspartic acid residues, as previously observed in a reflecting time-of-flight mass analyzer. In addition, preferential fragmentation was observed, for the first time, adjacent to glutamic acid residues. It is hypothesized that the long time-window of the present measurement (10-4 - 10-1 sec) favors the observation of low-energy, entropically-disfavored reactions at acidic residues. The preferential fragmentation at Asp and Glu residues observed in the ion trap MS has important practical implications. A paper describing these findings has been published in J. Am. Chem. Soc. 117, 5411-5412 (1995). .